Odel
MCP server: One MCP server.

DECIMER MCP Server

@docminusRun by its publisher: served from their own domain, namespace checked by the registry.MCP server · External

MCP server for DECIMER image-to-SMILES chemical structure recognition

Chemistryv0.1.4MITPython
Freeno charge per call
How to install

Runs on your machine from its package; the steps are below.

What it does

  1. Reads
  2. Writes
  3. High impact

At most: only reads or looks up information.

What it costs

Free

Odel charges nothing per call. The publisher may charge for its own service.

Runs locally over stdio

This server isn't hosted — your MCP client launches it from a package registry. Use one of the commands below, or drop the config into your client (e.g. Claude Desktop).

PyPIdecimer-mcp-serverv0.1.4

Run

uvx decimer-mcp-server

MCP client config

{
  "mcpServers": {
    "decimer-mcp-server": {
      "command": "uvx",
      "args": [
        "decimer-mcp-server"
      ]
    }
  }
}
README3 min read

mcp-name: io.github.DocMinus/decimer-mcp-server

MCP server that exposes DECIMER image-to-SMILES functionality as tool calls.

This project is a thin adapter over the existing FastAPI service in DecimerServerAPI. It does not run DECIMER models directly. The adapter sends JSON requests by default, with automatic fallback to form payloads for compatibility.

Tools

  • server_health: Checks whether the DECIMER FastAPI server is reachable.
  • analyze_chemical_image: Sends a base64-encoded image to /image2smiles/ and returns structured output.

Requirements

  • Python 3.10+
  • Running DECIMER API server (default: http://localhost:8099)

find it at either of these two versions:

Install

bash
cd /Users/a/dev/DecimerMCPServer
uv venv
uv sync

Configuration

Copy .env.example values into your environment:

  • DECIMER_API_BASE_URL (default http://localhost:8099)
  • DECIMER_API_TIMEOUT_SECONDS (default 60)
  • DECIMER_MAX_IMAGE_BYTES (default 10000000)
  • DECIMER_MCP_LOG_LEVEL (default INFO)

Run (stdio transport)

bash
uv run decimer-mcp-server

or

bash
uv run python -m decimer_mcp_server

Example MCP client config

json
{
  "mcpServers": {
    "decimer": {
      "command": "uv",
      "args": ["run", "python", "-m", "decimer_mcp_server"],
      "env": {
        "DECIMER_API_BASE_URL": "http://localhost:8099"
      }
    }
  }
}

Output shape

analyze_chemical_image returns:

json
{
  "ok": true,
  "smiles": "CCO",
  "reason": null,
  "api_status_code": 200,
  "api_message": null,
  "classifier_score": 0.0000012,
  "classifier_threshold": 0.3,
  "classifier_decision": "structure_like"
}

When no SMILES is returned by API classifier behavior:

json
{
  "ok": true,
  "smiles": null,
  "reason": "not_chemical_structure",
  "api_status_code": 200,
  "api_message": "No SMILES returned by API",
  "classifier_score": 0.99999,
  "classifier_threshold": 0.3,
  "classifier_decision": "not_structure_like"
}

Development tests

bash
uv sync --extra dev
uv run pytest

Make targets:

bash
make sync
make test

Smoke test helper

Run one health check + one inference call against your DECIMER API:

bash
cd /Users/a/dev/DecimerMCPServer
DECIMER_API_BASE_URL=http://chitchat:8099 uv run decimer-mcp-smoke-test --image /Users/a/dev/DecimerServerAPI/example_usage/structure.png

If you keep settings in .env, load it with:

bash
uv run --env-file .env decimer-mcp-smoke-test --image /Users/a/dev/DecimerServerAPI/example_usage/structure.png

or use make:

bash
make smoke

Override the image path if needed:

bash
make smoke SMOKE_IMAGE=/absolute/path/to/image.png

## MCP Registry publishing

Tags matching `v*` trigger `.github/workflows/publish-mcp.yml`.

Workflow steps:
- installs `mcp-publisher`
- validates `server.json`
- calls registry publish using secret `MCP_REGISTRY_TOKEN`
- publishes slug `io.github.DocMinus/decimer-mcp-server` (case sensitive; must match registry grant)

Before tagging:
1. Update `pyproject.toml` + `server.json` versions
2. Ensure `server.json` stays valid (`uv pip install jsonschema && python validate snippet from AGENTS.md`)
3. Add GitHub repo secret `MCP_REGISTRY_TOKEN` (GitHub PAT with `repo`, `workflow` scopes)

Release flow:
```bash
git tag v0.1.1
git push origin v0.1.1

Monitor Actions tab. If publish fails, rerun using workflow dispatch after fixing issues.


## Contribution
This project was built by DocMinus with AI-assisted coding support (OpenCode/Copilot-style tooling), then reviewed and tested by the author.

## AI usage policy

- AI assistance was used for scaffolding, implementation drafts, and documentation edits.
- Final technical decisions, validation runs, and acceptance were performed by the maintainer.
- Runtime behavior should be validated with local tests (`make test`) and smoke tests (`make smoke`) before release.

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